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Manganese in PDB 5ktl: Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.

Enzymatic activity of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.

All present enzymatic activity of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis., PDB code: 5ktl was solved by J.B.Christensen, S.Panjikar, M.Perugini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.92
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.727, 154.347, 55.795, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.2

Manganese Binding Sites:

The binding sites of Manganese atom in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. (pdb code 5ktl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis., PDB code: 5ktl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 5ktl

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Manganese binding site 1 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:34.4
occ:1.00
 OE1 A:GLN67 2.0 42.8 1.0
O A:HOH496 2.1 26.7 1.0
O A:HOH409 2.2 34.9 1.0
O A:HOH411 2.2 24.5 1.0
OE2 A:GLU64 2.2 25.2 1.0
O A:HOH515 2.5 40.6 1.0
CD A:GLU64 3.2 24.5 1.0
CD A:GLN67 3.3 44.3 1.0
OE1 A:GLU64 3.5 25.4 1.0
OG1 A:THR68 3.8 29.6 1.0
O A:HOH507 4.0 38.8 1.0
CG A:GLN67 4.2 43.1 1.0
NE2 A:GLN67 4.2 40.9 1.0
CG A:GLU64 4.6 22.6 1.0
CB A:ALA27 4.6 25.2 1.0
O A:GLU64 4.7 21.2 1.0

Manganese binding site 2 out of 7 in 5ktl

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Manganese binding site 2 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:60.5
occ:1.00
 O A:HOH520 2.2 58.1 1.0
OD1 A:ASP39 2.6 28.8 1.0
CG A:ASP39 3.4 30.4 1.0
O A:HOH404 3.7 36.0 1.0
CB A:ASP39 3.9 25.5 1.0
CA A:ASP39 4.2 23.7 1.0
OD2 A:ASP39 4.4 31.2 1.0
O A:HOH415 4.5 37.7 1.0

Manganese binding site 3 out of 7 in 5ktl

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Manganese binding site 3 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:65.6
occ:1.00
 MN A:MN304 2.3 90.6 1.0
O A:HOH402 2.5 32.5 1.0
OE1 A:GLU58 2.7 37.5 1.0
O A:HOH527 2.7 43.3 1.0
O A:HOH517 2.8 37.8 1.0
CD A:GLU58 3.4 32.1 1.0
OE2 A:GLU58 3.4 39.0 1.0
OE2 A:GLU86 4.4 45.0 1.0
OG A:SER50 4.5 24.6 1.0
O A:SER50 4.6 20.7 1.0
CE3 A:TRP55 4.7 36.6 1.0
O A:LEU53 4.7 23.8 1.0
CG A:GLU58 4.7 28.1 1.0

Manganese binding site 4 out of 7 in 5ktl

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Manganese binding site 4 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:90.6
occ:1.00
 O A:HOH402 1.9 32.5 1.0
MN A:MN303 2.3 65.6 1.0
O A:LEU53 2.6 23.8 1.0
OE2 A:GLU58 2.8 39.0 1.0
O A:SER50 2.9 20.7 1.0
CD A:GLU58 3.2 32.1 1.0
O A:HOH517 3.3 37.8 1.0
OE1 A:GLU58 3.4 37.5 1.0
C A:LEU53 3.6 23.8 1.0
C A:SER50 3.9 21.3 1.0
N A:LEU53 4.1 22.1 1.0
CA A:LEU53 4.2 22.2 1.0
CG A:GLU58 4.2 28.1 1.0
CB A:LEU53 4.2 24.4 1.0
OG A:SER50 4.2 24.6 1.0
C A:SER54 4.4 22.9 1.0
O A:SER54 4.4 20.4 1.0
O A:PRO51 4.5 22.9 1.0
C A:PRO51 4.5 23.0 1.0
N A:SER54 4.6 21.4 1.0
N A:TRP55 4.6 22.1 1.0
CA A:SER50 4.7 21.2 1.0
CA A:SER54 4.7 22.7 1.0
CA A:PRO51 4.7 21.6 1.0
N A:PRO51 4.9 20.9 1.0

Manganese binding site 5 out of 7 in 5ktl

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Manganese binding site 5 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:59.3
occ:1.00
 O B:HOH514 2.3 37.8 1.0
O B:HOH465 2.4 35.7 1.0
MN B:MN302 2.4 76.5 1.0
OE1 B:GLU58 2.5 42.8 1.0
CD B:GLU58 3.3 34.5 1.0
OE2 B:GLU58 3.4 41.9 1.0
O B:HOH515 3.9 38.9 1.0
OE2 B:GLU86 4.0 48.0 1.0
OG B:SER50 4.3 32.5 1.0
O B:SER50 4.5 23.7 1.0
CG B:GLU58 4.6 30.8 1.0
O B:LEU53 4.7 23.5 1.0
CE3 B:TRP55 5.0 39.1 1.0

Manganese binding site 6 out of 7 in 5ktl

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Manganese binding site 6 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:76.5
occ:1.00
 O B:SER50 2.4 23.7 1.0
MN B:MN301 2.4 59.3 1.0
O B:HOH465 2.5 35.7 1.0
O B:LEU53 2.8 23.5 1.0
O B:HOH514 3.2 37.8 1.0
OE2 B:GLU58 3.4 41.9 1.0
OE1 B:GLU58 3.4 42.8 1.0
C B:SER50 3.4 24.0 1.0
CD B:GLU58 3.5 34.5 1.0
C B:LEU53 3.8 23.2 1.0
OG B:SER50 3.9 32.5 1.0
N B:LEU53 4.0 22.1 1.0
C B:PRO51 4.2 25.1 1.0
O B:PRO51 4.2 27.0 1.0
CB B:LEU53 4.2 20.6 1.0
CA B:PRO51 4.2 24.8 1.0
CA B:LEU53 4.3 22.7 1.0
CA B:SER50 4.3 23.9 1.0
N B:PRO51 4.3 23.1 1.0
CG B:GLU58 4.5 30.8 1.0
CB B:SER50 4.7 25.6 1.0
N B:THR52 4.8 23.5 1.0
O B:HOH530 4.8 35.2 1.0
N B:SER54 4.8 24.0 1.0
C B:SER54 4.9 25.8 1.0
O B:SER54 4.9 21.6 1.0

Manganese binding site 7 out of 7 in 5ktl

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Manganese binding site 7 out of 7 in the Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Dihydrodipicolinate Synthase From the Industrial and Evolutionarily Important Cyanobacteria Anabaena Variabilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:67.8
occ:1.00
 O B:HOH518 2.3 52.1 1.0
NE2 B:HIS32 2.6 34.2 1.0
O B:HOH468 2.6 48.0 1.0
O B:HOH475 2.8 28.5 1.0
CE1 B:HIS32 3.5 35.6 1.0
CD2 B:HIS32 3.6 32.4 1.0
O B:HIS211 3.9 27.1 1.0
O B:HOH482 4.0 31.7 1.0
O B:HOH526 4.4 42.9 1.0
O B:LEU212 4.5 26.2 1.0
ND1 B:HIS32 4.7 36.7 1.0
CG B:HIS32 4.7 31.3 1.0
OE1 B:GLN262 4.8 36.8 1.0
CA B:LEU212 4.8 23.9 1.0
NE2 B:GLN262 4.9 34.4 1.0
C B:HIS211 4.9 24.9 1.0
C B:LEU212 4.9 24.6 1.0

Reference:

J.B.Christensen, T.P.Soares Da Costa, P.Faou, F.G.Pearce, S.Panjikar, M.A.Perugini. Structure and Function of Cyanobacterial Dhdps and Dhdpr. Sci Rep V. 6 37111 2016.
ISSN: ESSN 2045-2322
PubMed: 27845445
DOI: 10.1038/SREP37111
Page generated: Sun Oct 6 01:47:13 2024

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